Dear colleagues, I am very new to this so please forgive me if this question is too basic. I couldn't find an answer in the archive. I am trying to pre-process a large number of affy arrays and use the expression values in a linkage analysis for expression QTL mapping. I ran just.gcrma on the data because running ReadAffy then gcrma didn't work on so many arrays. It returned an exprSet object which has been normalised. But I have a feeling that the default quantile normalisation is not suitable for what I want to do. I think I can turn normalisation off, but then how do I apply other types of normalisation on an exprSet object? Expresso can only take an AffyBatch object, right? Cheers, Alex ------------------------------------ Alex Lam PhD student Department of Genetics and Genomics Roslin Institute (Edinburgh) Roslin Midlothian EH25 9PS Phone +44 131 5274471 Web http://www.roslin.ac.uk

I believe you can call just.gcrma() with a normalize=FALSE parameter to turn off the quantile normalization stage. If you have affyPLM loaded then you can use the normalize() method on an exprSet. The methods available are pretty much the same as those in the affy package for AffyBatch objects. The only thing to note is that you will have to tell it to transform your data back to natural scale, which is what most of the underlying normalization routines assume as input, if your expression values are in log2 scale. eg library(gcrma) library(affyPLM) eset <- justGCRMA(normalize=FALSE) eset.normalized <- normalize(eset,"contrast",transfn="antilog") On Tue, 2006-06-27 at 13:33 +0100, alex lam (RI) wrote: > Dear colleagues, > > I am very new to this so please forgive me if this question is too > basic. I couldn't find an answer in the archive. > > I am trying to pre-process a large number of affy arrays and use the > expression values in a linkage analysis for expression QTL mapping. I > ran just.gcrma on the data because running ReadAffy then gcrma didn't > work on so many arrays. It returned an exprSet object which has been > normalised. But I have a feeling that the default quantile normalisation > is not suitable for what I want to do. > > I think I can turn normalisation off, but then how do I apply other > types of normalisation on an exprSet object? Expresso can only take an > AffyBatch object, right? > > Cheers, > Alex > > ------------------------------------ > Alex Lam > PhD student > Department of Genetics and Genomics > Roslin Institute (Edinburgh) > Roslin > Midlothian EH25 9PS > > Phone +44 131 5274471 > Web http://www.roslin.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Ben Bolstad <bmb at="" bmbolstad.com=""> http://bmbolstad.com

For a list of normalization methods, check out the help for function "normalize" in "affy" package. The available methods can be viewed with "methods(normalize)". There are invididual help files for each method listed Here's what I saw: > methods(normalize) [1] normalize.AffyBatch.constant normalize.AffyBatch.contrasts [3] normalize.AffyBatch.invariantset normalize.AffyBatch.loess [5] normalize.AffyBatch.qspline normalize.AffyBatch.quantiles [7] normalize.AffyBatch.quantiles.robust normalize.constant [9] normalize.invariantset normalize.loess [11] normalize.methods normalize.qspline [13] normalize.quantiles normalize.quantiles.robust cheers, Jean On Tue, 27 Jun 2006, alex lam (RI) wrote: > > Dear colleagues, > > I am very new to this so please forgive me if this question is too > basic. I couldn't find an answer in the archive. > > I am trying to pre-process a large number of affy arrays and use the > expression values in a linkage analysis for expression QTL mapping. I > ran just.gcrma on the data because running ReadAffy then gcrma didn't > work on so many arrays. It returned an exprSet object which has been > normalised. But I have a feeling that the default quantile normalisation > is not suitable for what I want to do. > > I think I can turn normalisation off, but then how do I apply other > types of normalisation on an exprSet object? Expresso can only take an > AffyBatch object, right? > > Cheers, > Alex > > ------------------------------------ > Alex Lam > PhD student > Department of Genetics and Genomics > Roslin Institute (Edinburgh) > Roslin > Midlothian EH25 9PS > > Phone +44 131 5274471 > Web http://www.roslin.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >